Specifically, similarity of binding sites is assessed by considering the sites' sequence and structure conservation as well as physicochemical properties of protein assemblies.
Finally, statistical significance of the spatial clustering of positively selected amino acids and correspondence with functional binding sites was assessed using programs from Clark and Swanson [ 78].
The anti-invasive potential of M6P/IGF2R forms lacking individual M6P-binding sites was assessed by Matrigel invasion assays.
ChIP-seq of H3.3 was performed in WT and ATRX KO mouse ESCs, and ATRX-binding sites were assessed for H3.3 enrichment.
To determine the distribution of specific glyco-receptors that might mediate the functions of this glycan-binding protein, Gal-1-binding sites were assessed by flow cytometry of mouse enterocytes using biotinylated rGal-1.
The presence of recognized DNA binding motifs and active sites was assessed by using the Expasy site and PFAM bioinformatics algorithms available at http://us.expasy.org/cgi-bin/protscale.pl, and the electrostatic charge was calculated by using the EMBOSS package (http://proteas.uio.no/EMBOSS).uio.no/EMBOSS
This is where a DNA-binding protein is immunoprecipitated with its cognate DNA and the presence of DNA binding at a specific site is assessed by quantitative PCR.
The relevance of this site was assessed by measuring effects of mutations on autophosphorylation, kinase activity, GTP binding, GTP hydrolysis, and LRRK2 multimerization.
These binding sites are highly charged.
